comparison replace_text_in_line.xml @ 12:a6f147a050a2 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8

11:74a8bef53a00

<tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.1">
    <description>in entire line</description>
    <macros>
	<import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="4.4">sed</requirement>
    </requirements>
    <version_command>sed --version | head -n 1</version_command>
    <command>
<![CDATA[
	 sed
      -r
      --sandbox
      's/$find_pattern/$replace_pattern/g'
      '$infile'
      > '$outfile'
]]>

    </command>
    <inputs>
	<param format="txt" name="infile" type="data" label="File to process" />
         <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&#39;"/>
                    <remove value="/"/>

                <mapping initial="none">
                    <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
                    <add source="/" target="\/"/>
                </mapping>
            </sanitizer>
        </param>
         <param name="replace_pattern" type="text" size="20" label="Replace with:" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&#39;"/>
                    <remove value="/"/>

                </mapping>

            </sanitizer>

        </param>
    </inputs>
    <outputs>
	<data name="outfile" format_source="infile" metadata_source="infile"/>
    </outputs>
    <tests>
	<test>
            <param name="infile" value="replace_text_in_line1.txt" />
            <param name="find_pattern" value="CTC." />
            <param name="replace_pattern" value="FOOBAR" />
            <output name="outfile" file="replace_text_in_line_results1.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

-----

**Examples of Find Patterns**

- **HELLO**     The word 'HELLO' (case sensitive).
- **AG.T**	The letters A,G followed by any single character, followed by the letter T.
- **A{4,}**     Four or more consecutive A's.
- **chr2[012]\\t**	 The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
- **hsa-mir-([^ ]+)**        The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern.


**Examples of Replace Patterns**

Find the first four characters in each line, and replace them with the same text, followed by a tab character. In practice - this will split the first line into two columns.


-----

**Extened Regular Expression Syntax**

The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.

- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
- **^** matches the beginning of a string(but not an internal line).

12:a6f147a050a2

<tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.2">
    <description>in entire line</description>
    <macros>
       <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="4.4">sed</requirement>
    </requirements>
    <version_command>sed --version | head -n 1</version_command>
    <command>
<![CDATA[
   sed
      -r
      --sandbox
      #for $replacement in $replacements:
        -e
        's/$replacement.find_pattern/$replacement.replace_pattern/g'
      #end for
      '$infile'
      > '$outfile'
]]>

    </command>
    <inputs>
      <param format="txt" name="infile" type="data" label="File to process" />
      <repeat name="replacements" title="Replacement" min="1">
         <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&#39;"/>
                    <remove value="/"/>

                <mapping initial="none">
                    <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
                    <add source="/" target="\/"/>
                </mapping>
            </sanitizer>
         </param>
         <param name="replace_pattern" type="text" size="20" label="Replace with:" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&#39;"/>
                    <remove value="/"/>

                </mapping>

            </sanitizer>

        </param>
      </repeat>
    </inputs>
    <outputs>
  <data name="outfile" format_source="infile" metadata_source="infile"/>
    </outputs>
    <tests>
         <test>
            <param name="infile" value="replace_text_in_line1.txt" />
            <param name="find_pattern" value="CTC." />
            <param name="replace_pattern" value="FOOBAR" />
            <output name="outfile" file="replace_text_in_line_results1.txt" />
        </test>
        <test>
            <param name="infile" value="replace_text_in_line1.txt" />
            <repeat name="replacements">
              <param name="find_pattern" value="CTC." />
              <param name="replace_pattern" value="FOOBAR" />
            </repeat>
            <repeat name="replacements">
              <param name="find_pattern" value="chr" />
              <param name="replace_pattern" value="domain" />
            </repeat>
            <output name="outfile" file="replace_text_in_line_results2.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

-----

**Examples of Find Patterns**

- **HELLO**     The word 'HELLO' (case sensitive).
- **AG.T**  The letters A,G followed by any single character, followed by the letter T.
- **A{4,}**     Four or more consecutive A's.
- **chr2[012]\\t**   The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
- **hsa-mir-([^ ]+)**        The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern.


**Examples of Replace Patterns**

Find the first four characters in each line, and replace them with the same text, followed by a tab character. In practice - this will split the first line into two columns.


-----

**Extended Regular Expression Syntax**

The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.

- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
- **^** matches the beginning of a string(but not an internal line).